RetrogeneDB ID: retro_eeur_356

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_268982:4030..4872(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CSGALNACT1
• Ensembl ID: ENSEEUG00000007709
• Aliases: None
• Description: chondroitin sulfate N-acetylgalactosaminyltransferase 1 [Source:HGNC Symbol;Acc:24290]

Sequence

>retro_eeur_356
GTGAGGATGATTCGCCGGGGACTGCTGTCGTGGGTCTCGAGGGTGGCAGTGCTGCTTGTTCTCCTTTGCTGTGTCATCTC
CGTCCTCTACTTGCTGGCCTGCACCCCAAAAGACAACGAGGAGCAGCTGGGACTTCCCTGGGCCAATGGCCCCATAGGGA
AAGAAGGGTACCAGGCTGTCCTGCAGGAGTGGGAAGAGCAGCACCGCAACTATATCAGCAGCCTCAAGCGGCAGATCTTG
CAGCTCAAAGAGGAGCTGCAGGAGAGGAGCACGCAACTCAAGTATGCGCAGCAACAGGCCAGTGACCCTGCGGGCCTGGA
TCCAGGCCCCCCGGAGAAGACCCAGGCCGACCTGCTGGCCTTCTTGCACTCCCAGGTGGAGAGGGCGGAGGTGCATGCCG
GTGTCAAGCTGGCCACTGAGTATGCAGCCGTGCCTTTCGACAGTTTCACCCTGCAGAAAGTGTACCAATTAGAGACTGGC
CTGACTCGCCACCCCGAGGAAAAGCCAGTGAGGAAAGATAAGCGGGATGAACTGGTGGAAGCCATGGAATCTGCTCTGGA
GACCTTGAACAGCCCGGAGAAGAGCAGCCCCCATCACCGTCCTTACACCTCTTCGGATTTCATAGAAGGGATCTACCGAA
CGGAAAAGGATAAAGGCACTTTGTATGAGCTCACATTCAAAGGGGACCACAAGCATGAATTCAGAAGACTTATCTTGTTT
CGACCTTTTTGCCCCATCATGAAAGTGAAAAAGAACGACTCAACATGGCCAATATACTTATCAACGTGATCGTGCCGCTA
GCAAAGAGAGTGGACAAGTTCCAGCAGTTCATGCAGAATTTC

Alignment

ORF - retro_eeur_356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.33 %
• Parental protein coverage: 53.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRMIRRGLLSWVSRVAVLLVLLCCVISVLYLLACTPKGNEEQLGLPWANGPTGKEGYQAVLQEWEEQHRN
          VRMIRRGLLSWVSRVAVLLVLLCCVISVLYLLACTPK.NEEQLGLPWANGP.GKEGYQAVLQEWEEQHRN
Retrocopy VRMIRRGLLSWVSRVAVLLVLLCCVISVLYLLACTPKDNEEQLGLPWANGPIGKEGYQAVLQEWEEQHRN

Parental  YISSLKRQISQLKEELQERSTQLKNAQQQASDPAGLDPGPPEKTQADLLAFLHSQVERAEVHAGVKLATE
          YISSLKRQI.QLKEELQERSTQLK.AQQQASDPAGLDPGPPEKTQADLLAFLHSQVERAEVHAGVKLATE
Retrocopy YISSLKRQILQLKEELQERSTQLKYAQQQASDPAGLDPGPPEKTQADLLAFLHSQVERAEVHAGVKLATE

Parental  YAAVPCDEGALQKVYQLETGLAGHPEEKPVRKDKRDELVEAIESALETLNSPEESSPHHRPYTSSDFIEG
          YAAVP.D...LQKVYQLETGL..HPEEKPVRKDKRDELVEA.ESALETLNSPE.SSPHHRPYTSSDFIEG
Retrocopy YAAVPFDSFTLQKVYQLETGLTRHPEEKPVRKDKRDELVEAMESALETLNSPEKSSPHHRPYTSSDFIEG

Parental  IYRTEKDKGTLYELTFKGDHKHEFRRLILFRPFGPIMKVK-KERLNMANTLINVIVPLAKRVDKFRQFMQ
          IYRTEKDKGTLYELTFKGDHKHEFRRLILFRPF.PIMKVK.KERLNMAN.LINVIVPLAKRVDKF.QFMQ
Retrocopy IYRTEKDKGTLYELTFKGDHKHEFRRLILFRPFCPIMKVK<KERLNMANILINVIVPLAKRVDKFQQFMQ

Parental  NF
          NF
Retrocopy NF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	5.00 RPM	10.15 RPM
SRP017611_kidney	0.38 RPM	1.69 RPM
SRP017611_liver	0.16 RPM	0.64 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_356 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007709	1 retrocopy	retro_eeur_356 ,